Wow, that's a lot of ideas. Good job getting this all together.
My thoughts, going down the list:
The Roles of Magic:
I think we should use all of these, to some extent. Though the Fire Wand is not such a great idea, as it shares functions with the crossbow, but I understand it's just an example. That earth gem sounds like a lot of fun. Just the ability to turn soil into stone would be great.
Miracles would go with the religion system, which I'm not going to discuss much here because I'm of the opinion that Divine magic should be separate and different from Arcane magic.
Technology is awesome and fits with the feel of DF.
The Wielder of Miracle:
I think there should probably be two levels of magic users. The first should be like what you call the Spell-casters and Magicians. There should be different skills related to magic. Runecrafting and a channeling skill for each sphere, at least. This would happen in workshops, and getting someone good at it would be difficult. This would allow enhancement of items beyond just increasing value, primarily. It would also allow magic based traps.
Minor stuff from the Technology section above could be made this way. Channeling energy could, perhaps, be used for the Miracle topic there.
The other magic users would be more akin to what you call a Sage. (What you refer to as a Wizard, I'd call a demigod and mix it in with the religious system).
The sage like pretty much as you said, and should be the only one to get combat-usable magic. Even so, it should be grand in scope and preparation time. Perhaps a sudden inferno takes out a squad of goblins, but it most be invoked through a summoning circle and takes a long time to prepare. These guys would create the components for the larger-scale things listed in Technology, such as your Portal and Golems.
The Source of Magic:
I think it should use a few of your options. For sages:
It is physically draining (as per Stamina/Vitality) but an Attribute modifies just how draining it is.
Other magic-users won't be directly channeling magic, and thus that wouldn't apply to them.
All mages would use magic from outside sources, whether through Animism (which ties in very well with spheres) or through Leylines and Nodes (which is generally what your Rivers and pools of magic would be referred to.)
Of those options, I'd prefer Animism. Magic can be draw upon anywhere, but spheres effect it. In a life sphere, for example, you would be unable to channel death magic, but Life magic would be stronger ad easier to channel.
Magical Environments:
This is Spheres. Toady already has plans for that.